# DeCo-MIL: Debiased Counterfactual Reasoning for Long-Tailed Whole Slide Image Analysis

arXiv: https://arxiv.org/abs/2608.14719 · HTML: https://mlsanity.com/paper/2608.14719/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 25 references that are in the map.
- First posted on arXiv 12 Aug 2026.

## Builds on (most cited first, 21 of 21)

- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- [Visualizing and Understanding Convolutional Networks](https://mlsanity.com/paper/1311.2901/) (2013)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Decoupling Representation and Classifier for Long-Tailed Recognition](https://mlsanity.com/paper/1910.09217/) (2019)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Long-tail learning via logit adjustment](https://mlsanity.com/paper/2007.07314/) (2020)
- [Interpretable Explanations of Black Boxes by Meaningful Perturbation](https://mlsanity.com/paper/1704.03296/) (2017)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Balanced Meta-Softmax for Long-Tailed Visual Recognition](https://mlsanity.com/paper/2007.10740/) (2020)
- [Long-tailed Recognition by Routing Diverse Distribution-Aware Experts](https://mlsanity.com/paper/2010.01809/) (2020)
- [Long-Tailed Classification by Keeping the Good and Removing the Bad Momentum Causal Effect](https://mlsanity.com/paper/2009.12991/) (2020)
- [Remix: Rebalanced Mixup](https://mlsanity.com/paper/2007.03943/) (2020)
- [Counterfactual Attention Learning for Fine-Grained Visual Categorization and Re-identification](https://mlsanity.com/paper/2108.08728/) (2021)
- [Interventional Bag Multi-Instance Learning On Whole-Slide Pathological Images](https://mlsanity.com/paper/2303.06873/) (2023)
- [Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology](https://mlsanity.com/paper/2405.11643/) (2024)
- [Dynamic Graph Representation with Knowledge-aware Attention for Histopathology Whole Slide Image Analysis](https://mlsanity.com/paper/2403.07719/) (2024)
- [Agent Aggregator with Mask Denoise Mechanism for Histopathology Whole Slide Image Analysis](https://mlsanity.com/paper/2409.11664/) (2024)
- [MiCo: Multiple Instance Learning with Context-Aware Clustering for Whole Slide Image Analysis](https://mlsanity.com/paper/2506.18028/) (2025)
- [SC-MIL: Supervised Contrastive Multiple Instance Learning for Imbalanced Classification in Pathology](https://mlsanity.com/paper/2303.13405/) (2023)
- [Multimodal Distillation-Driven Ensemble Learning for Long-Tailed Histopathology Whole Slide Images Analysis](https://mlsanity.com/paper/2503.00915/) (2025)

## Abstract (arXiv)

Multiple instance learning (MIL) is widely used for weakly supervised whole slide image (WSI) analysis. However, under long-tailed distributions, MIL-based WSI analysis faces a nested dual long-tail: an inter-slide class long tail and an intra-slide long tail of instance-level discriminative evidence. The two long tails are coupled: tail classes have few training slides, while their limited diagnostic evidence is concentrated in a few patches and obscured by abundant within-bag redundancy. This coupling biases models toward head classes and degrades rare-class recognition. To address this, we propose DeCo-MIL for long-tailed WSI analysis, which jointly alleviates the nested dual long-tail through frequency-debiased counterfactual reasoning. For the inner long tail, DeCo-MIL clusters patches into tissue-morphology anchors, replaces each anchor with its matched normal prototype to perform a counterfactual intervention, and estimates its counterfactual contribution to the ground-truth class using class-frequency-corrected predictions. These contributions guide redundancy masking to preserve scarce discriminative instances. For the outer long tail, DeCo-MIL constructs anchor-stratified pseudo-bags from redundancy-reduced bags and combines tail-aware oversampling with consistency regularization, increasing effective supervision for tail classes while preserving tissue-morphology composition. Extensive experiments on three long-tailed WSI benchmarks demonstrate that DeCo-MIL achieves state-of-the-art performance in both tail-class recognition and overall classification.